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Background  tRNase Z removes the 3'-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase Z S ) and long (tRNase Z L ) forms. Based on the sequence characteristics, they can be divided into two major types: bacterial-type tRNase Z S  and eukaryotic-type tRNase Z L , and one minor type,  Thermotoga maritima  (TM)-type tRNase Z S . The number of tRNase Zs is highly variable, with the largest number being identified experimentally in the flowering plant  Arabidopsis thaliana . It is unknown whether multiple tRNase Zs found in  A. thaliana  is common to the plant kingdom. Also unknown is the extent of sequence and structural conservation among tRNase Zs from the plant kingdom.    Results  We report the identification and analysis of candidate tRNase Zs in 27 fully sequenced genomes of green plants, the great majority of which are flowering plants. It appears that green plants contain multiple distinct tRNase Zs predicted to reside in different subcellular compartments. Furthermore, while the bacterial-type tRNase Z S s are present only in basal land plants and green algae, the TM-type tRNase Z S s are widespread in green plants. The protein sequences of the TM-type tRNase Z S s identified in green plants are similar to those of the bacterial-type tRNase Z S s but have distinct features, including the TM-type flexible arm, the variant catalytic HEAT and HST motifs, and a lack of the PxKxRN motif involved in CCA anti-determination (inhibition of tRNase Z activity by CCA), which prevents tRNase Z cleavage of mature tRNAs. Examination of flowering plant chloroplast tRNA genes reveals that many of these genes encode partial CCA sequences. Based on our results and previous studies, we predict that the plant TM-type tRNase Z S s may not recognize the CCA sequence as an anti-determinant.    Conclusions  Our findings substantially expand the current repertoire of the TM-type tRNase Z S s and hint at the possibility that these proteins may have been selected for their ability to process chloroplast pre-tRNAs with whole or partial CCA sequences. Our results also support the coevolution of tRNase Zs and tRNA 3'-trailer sequences in plants.

A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2